Literature DB >> 17967545

2dx_merge: data management and merging for 2D crystal images.

Bryant Gipson1, Xiangyan Zeng, Henning Stahlberg.   

Abstract

Electron crystallography of membrane proteins determines the structure of membrane-reconstituted and two-dimensionally (2D) crystallized membrane proteins by low-dose imaging with the transmission electron microscope, and computer image processing. We have previously presented the software system 2dx, for user-friendly image processing of 2D crystal images. Its central component 2dx_image is based on the MRC program suite, and allows the optionally fully automatic processing of one 2D crystal image. We present here the program 2dx_merge, which assists the user in the management of a 2D crystal image processing project, and facilitates the merging of the data from multiple images. The merged dataset can be used as a reference to re-process all images, which usually improves the resolution of the final reconstruction. Image processing and merging can be applied iteratively, until convergence is reached. 2dx is available under the GNU General Public License at http://2dx.org.

Mesh:

Year:  2007        PMID: 17967545      PMCID: PMC2157552          DOI: 10.1016/j.jsb.2007.09.011

Source DB:  PubMed          Journal:  J Struct Biol        ISSN: 1047-8477            Impact factor:   2.867


  19 in total

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Journal:  FEBS Lett       Date:  2001-08-31       Impact factor: 4.124

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Authors:  Ansgar Philippsen; Andreas D Schenk; Henning Stahlberg; Andreas Engel
Journal:  J Struct Biol       Date:  2003 Oct-Nov       Impact factor: 2.867

5.  Improved specimen preparation for cryo-electron microscopy using a symmetric carbon sandwich technique.

Authors:  Nobuhiko Gyobu; Kazutoshi Tani; Yoko Hiroaki; Akiko Kamegawa; Kaoru Mitsuoka; Yoshinori Fujiyoshi
Journal:  J Struct Biol       Date:  2004-06       Impact factor: 2.867

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Authors:  W Kühlbrandt
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Authors:  Xiangyan Zeng; Bryant Gipson; Zi Yan Zheng; Ludovic Renault; Henning Stahlberg
Journal:  J Struct Biol       Date:  2007-08-24       Impact factor: 2.867

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Authors:  H-W Rémigy; D Caujolle-Bert; K Suda; A Schenk; M Chami; A Engel
Journal:  FEBS Lett       Date:  2003-11-27       Impact factor: 4.124

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Authors:  Xiangyan Zeng; Henning Stahlberg; Nikolaus Grigorieff
Journal:  J Struct Biol       Date:  2007-09-25       Impact factor: 2.867

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  23 in total

1.  The Protein Structure Initiative Structural Biology Knowledgebase Technology Portal: a structural biology web resource.

Authors:  Lida K Gifford; Lester G Carter; Margaret J Gabanyi; Helen M Berman; Paul D Adams
Journal:  J Struct Funct Genomics       Date:  2012-04-06

2.  SbsB structure and lattice reconstruction unveil Ca2+ triggered S-layer assembly.

Authors:  Ekaterina Baranova; Rémi Fronzes; Abel Garcia-Pino; Nani Van Gerven; David Papapostolou; Gérard Péhau-Arnaudet; Els Pardon; Jan Steyaert; Stefan Howorka; Han Remaut
Journal:  Nature       Date:  2012-07-05       Impact factor: 49.962

3.  Sample Preparation and Data Collection for Electron Crystallographic Studies on Membrane Protein Structures and Lipid-Protein Interaction.

Authors:  Ka-Yi Chan; Chloe Du Truong; Yu-Ping Poh; Po-Lin Chiu
Journal:  Methods Mol Biol       Date:  2021

4.  Evaluation of super-resolution performance of the K2 electron-counting camera using 2D crystals of aquaporin-0.

Authors:  Po-Lin Chiu; Xueming Li; Zongli Li; Brian Beckett; Axel F Brilot; Nikolaus Grigorieff; David A Agard; Yifan Cheng; Thomas Walz
Journal:  J Struct Biol       Date:  2015-08-28       Impact factor: 2.867

5.  Growth of large and highly ordered 2D crystals of a K⁺ channel, structural role of lipidic environment.

Authors:  Rita De Zorzi; William V Nicholson; Jean-Michel Guigner; Françoise Erne-Brand; Catherine Vénien-Bryan
Journal:  Biophys J       Date:  2013-07-16       Impact factor: 4.033

6.  High-resolution low-dose scanning transmission electron microscopy.

Authors:  James P Buban; Quentin Ramasse; Bryant Gipson; Nigel D Browning; Henning Stahlberg
Journal:  J Electron Microsc (Tokyo)       Date:  2009-11-14

7.  Structural basis for receptor recognition and pore formation of a zebrafish aerolysin-like protein.

Authors:  Ning Jia; Nan Liu; Wang Cheng; Yong-Liang Jiang; Hui Sun; Lan-Lan Chen; Junhui Peng; Yonghui Zhang; Yue-He Ding; Zhi-Hui Zhang; Xuejuan Wang; Gang Cai; Junfeng Wang; Meng-Qiu Dong; Zhiyong Zhang; Hui Wu; Hong-Wei Wang; Yuxing Chen; Cong-Zhao Zhou
Journal:  EMBO Rep       Date:  2015-12-28       Impact factor: 8.807

8.  Deducing the symmetry of helical assemblies: Applications to membrane proteins.

Authors:  Nicolas Coudray; Ralph Lasala; Zhening Zhang; Kathy M Clark; Mark E Dumont; David L Stokes
Journal:  J Struct Biol       Date:  2016-05-30       Impact factor: 2.867

9.  Coassembly of Mgm1 isoforms requires cardiolipin and mediates mitochondrial inner membrane fusion.

Authors:  Rachel M DeVay; Lenin Dominguez-Ramirez; Laura L Lackner; Suzanne Hoppins; Henning Stahlberg; Jodi Nunnari
Journal:  J Cell Biol       Date:  2009-09-14       Impact factor: 10.539

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Authors:  Henning Stahlberg; Thomas Walz
Journal:  ACS Chem Biol       Date:  2008-05-16       Impact factor: 5.100

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